FIX: Fixing docs

Author: larsoner

doc/sphinxext/gen_rst.py

@@ -148,59 +148,50 @@ def generate_file_rst(fname, target_dir, src_dir, plot_gallery):
     this_template = rst_template
     last_dir = os.path.split(src_dir)[-1]
     # to avoid leading . in file names
-    if last_dir == '.': last_dir = ''
-    else: last_dir += '_'
-    short_fname =  last_dir + fname
+    if last_dir == '.':
+        last_dir = ''
+    else:
+        last_dir += '_'
+    short_fname = last_dir + fname
     src_file = os.path.join(src_dir, fname)
     example_file = os.path.join(target_dir, fname)
     shutil.copyfile(src_file, example_file)
     if plot_gallery and fname.startswith('plot'):
         # generate the plot as png image if file name
         # starts with plot and if it is more recent than an
         # existing image.
-        if not os.path.exists(
-                            os.path.join(target_dir, 'images')):
+        if not os.path.exists(os.path.join(target_dir, 'images')):
             os.makedirs(os.path.join(target_dir, 'images'))
         image_file = os.path.join(target_dir, 'images', image_name)
         if (not os.path.exists(image_file) or
-                os.stat(image_file).st_mtime <=
-                    os.stat(src_file).st_mtime):
+                os.stat(image_file).st_mtime <= os.stat(src_file).st_mtime):
             print 'plotting %s' % fname
             import matplotlib.pyplot as plt
             plt.close('all')
             try:
-                try:
-                    from mayavi import mlab
-                except ImportError:
-                    from enthought.mayavi import mlab
-                mlab.close(all=True)
-            except:
-                pass
-
-            try:
-                execfile(example_file, {'pl' : plt})
-                facecolor = plt.gcf().get_facecolor() # hack to keep black bg
+                brain = None
+                global plt
+                global brain
+                execfile(example_file, globals())
+                facecolor = plt.gcf().get_facecolor()  # hack to keep black bg
                 if facecolor == (0.0, 0.0, 0.0, 1.0):
                     plt.savefig(image_file, facecolor='black')
                 else:
                     plt.savefig(image_file)
 
-                try:
-                    brain.save_image(image_file)
-                except:
-                    pass
+                brain.save_image(image_file)
 
             except:
-                print 80*'_'
+                print 80 * '_'
                 print '%s is not compiling:' % fname
                 traceback.print_exc()
-                print 80*'_'
+                print 80 * '_'
         this_template = plot_rst_template
 
     docstring, short_desc, end_row = extract_docstring(example_file)
 
-    f = open(os.path.join(target_dir, fname[:-2] + 'rst'),'w')
-    f.write( this_template % locals())
+    f = open(os.path.join(target_dir, fname[:-2] + 'rst'), 'w')
+    f.write(this_template % locals())
     f.flush()
 
 

doc/surfer.cfg

@@ -1,4 +1,6 @@
 [visual]
+width=600
+height=600
 background=black
 cortex=classic
 default_view=lateral

examples/example_data/index.rst

@@ -3,8 +3,7 @@
 from warnings import warn
 
 import numpy as np
-from scipy import stats
-from scipy import ndimage
+from scipy import stats, ndimage, misc
 from matplotlib.colors import colorConverter
 
 import nibabel as nib
@@ -1697,7 +1696,7 @@ def close(self):
             self._v = None
 
     def __del__(self):
-        if self._v is not None:
+        if hasattr(self, '_v') and self._v is not None:
             self._v.dispose()
             self._v = None
 
@@ -1760,8 +1759,7 @@ def save_image(self, filename):
         a Mayavi figure to plot instead of TraitsUI) if you intend to
         script plotting commands.
         """
-        data = self.screenshot()
-        make_montage(filename, [data])
+        misc.imsave(filename, self.screenshot())
 
     def screenshot(self, mode='rgb', antialiased=False):
         """Generate a screenshot of current view
@@ -1796,7 +1794,8 @@ def screenshot(self, mode='rgb', antialiased=False):
         row = []
         for ri in range(self.brain_matrix.shape[0]):
             col = []
-            for ci in range(self.brain_matrix.shape[1]):
+            n_col = 2 if self._hemi == 'split' else 1
+            for ci in range(n_col):
                 col += [self.screenshot_single(mode, antialiased,
                                                ri, ci)]
             row += [np.concatenate(col, axis=1)]